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What’s a virus, anyway? Part 1: The bare-bones basics

Author Bruce Goldman

Published on April 2, 2020

As the coronavirus pandemic spreads across the globe, the term “virus” gets a lot of airplay. But what exactly are viruses, and how do they spread? Here’s a primer, with a hat tip to Stanford virologist Jan Carette, PhD.

For starters, viruses are easily the most abundant life form on Earth, if you accept the proposition that they’re alive. Try multiplying a billion by a billion, then multiply that by ten trillion, and that (10 to the 31st power) is the mind-numbing estimate of how many individual viral particles are estimated to populate the planet.

Is a virus a living thing? Maybe. Sometimes. It depends on location. “Outside of a cell, a viral particle is inert,” Carette told me. On its own, it can’t reproduce itself or, for that matter, produce anything at all. It’s the ultimate parasite.

Or, you could say more charitably, very efficient. Viruses travel light, packing only the baggage they absolutely need to hack into a cell, commandeer its molecular machinery, multiply and make an escape.

When it comes to viruses, there are exceptions to nearly every rule. But they do have things in common, said Carette.

A virus’s travel kit always includes its genome and a surrounding protein shell, or capsid, which keeps the viral genome safe, helps the virus latch onto cells and climb inside and, on occasion, abets its offspring’s getaway. The capsid consists of identical protein subunits, whose unique shapes and properties determine the capsid’s structure and function.

Some viruses also wear greasy overcoats, called envelopes, made from stolen shards of the membranes of the last cell they infected. Influenza and hepatitis C viruses have envelopes, as do coronaviruses, herpesviruses and HIV. Rhinoviruses, which are responsible for most common colds, and polioviruses don’t. Here’s a practical takeaway: Enveloped viruses particularly despise soap because it disrupts greasy membranes. Soap and water are to these viruses what exhaling garlic is to a vampire, which is why washing your hands works wonders.

How do viruses enter cells, replicate and head for the exits?

For a virus to spread, it must first find a way into a cell. But, said Carette, “penetrating a cell’s perimeter isn’t easy.” Cells’ outer membranes are normally tough to penetrate without some kind of special pass. But viruses have ways of tricking cells into letting them in. Typically, a portion of the viral capsid will have a strong affinity to bind with one or another protein dotting the surfaces of one or another particular cell type. The binding of the viral capsid with that cell-surface protein serves as an admission ticket, easing the virus’s invasion of the cell.

The viral genome, like ours, is an instruction kit for the production of proteins the virus needs. This genome can be made up of either DNA, as is the case with virtually all other creatures, or its close chemical relative RNA, which encodes genetic information just as DNA does but is much more flexible and somewhat less stable. Most mammal-infecting viruses’ genomes are made of RNA. (Not herpesviruses, though.)

In addition to the gene coding for its capsid protein, every virus needs another gene for its own version of an enzyme known as a polymerase. Inside the cell, viral polymerases generate numerous copies of the invader’s genes, from whose instructions the cell’s obedient molecular assembly line produces capsid subunits and other viral proteins.

Capsids — a virus’s protein shell — self-assemble from their subunits, often with help from proteins originally made by the cell for other purposes, but co-opted by the virus. These fresh copies of the viral genome are packaged inside newly-made capsids for export.

Viral genomes can also contain genes for proteins that can co-opt the cellular machinery to help viruses replicate and escape, or that can tweak the virus’s own genome — or ours. The genome can contain as few as two genes — one for the protein from which the capsid is built, the other for the polymerase — or as many as hundreds (as in herpesviruses, for example).

Often, the virus’s plentiful progeny punish the good deed of the cell that produced them by lysing it — punching holes in its outer membrane, busting out of it and destroying the cell in the process. But enveloped viruses can escape by an alternative process called budding, whereby they wrap themselves in a piece of membrane from the infected cell and, in these newly acquired greasy overcoats, diffuse through the cell’s outer membrane without structurally damaging it. Even then, the cell, having birthed myriad baby viruses, is often left fatally weakened.

Graphic illustration of a measles virus from the Centers for Disease Control and Prevention

What Is a Virus?

A virus is genetic material contained within an organic particle that invades living cells and uses their host’s metabolic processes to produce a new generation of viral particles.

The way they do this varies. Some insert their genetic material into the host’s DNA, where it can sit in wait until it’s translated at a later date. As the host cell replicates itself, it can make new viruses.

Viruses can also burst their host cell as they expand in numbers, in what’s called a lytic cycle of reproduction.

How big are viruses?

The word virus comes from a Latin word describing poisonous liquids. This is because early forms of isolating and imaging microbes couldn’t capture such tiny particles.

Virus sizes vary from the extremely minuscule – 17 nanometre wide Porcine Circovirus, for example – to monsters that challenge the very definition of ‘virus’, such as the 2.3 micrometre Tupanvirus.

Similarly, they come in a range of complexities, containing different proteins or surrounded by an array of shells and envelopes to assist in their infection and reproduction of just about every species across every kingdom of life.

Viruses can be encoded in a variety of ways. Rotaviruses are based on a double strand of RNA, for example. Coronaviruses have a single strand of RNA, which is ‘positive sense’, as in it can be translated directly into new proteins. Influenza has negative sense RNA, meaning it needs an extra transcribing step before it can make proteins.

Smallpox and herpes viruses are examples of DNA viruses, which force the host to transcribe its genome into RNA on entry.

Sizes of these genomes also vary. Some of the largest can be over a million base pairs long. On the other hand, an RNA virus that infects bacteria, called MS2, has barely 3,500 base pairs.

It’s impossible to know with certainty just how many types of viruses exist in the natural world, with numbers climbing as researchers use new tools to search for classified and unknown genetic signatures in the soil, oceans, and even the skies. Rough estimates suggest there could be as many as 100 million types of virus on Earth’s surface.

Are viruses alive?

This is a question scientists continue to discuss as definitions of life and ecology change. Current thinking suggests viruses should be considered part of a complex living system, one that extends between all organisms.

‘Virions’ are the inactive particles that move through the environment, which we don’t tend to think of as alive. Only once they’re part of a cell do viruses take on living characteristics of their own, borrowing the host’s biochemistry to reproduce.

As such, it’s more accurate to think of viruses as part of the continuum between chemistry and biology, one that isn’t clearly divided into living and non-living.

How Viruses Work and How to Prevent and Eliminate Them Naturally

We have identified more than
2,000 viruses, though only 10% infect humans. Scientists used to think
human viruses do not affect animals and animal viruses do not affect
humans, but we now know that viruses not only jump species, sometimes
they combine to create new strains. New strains can present a clear
threat to human survival.

In 1918 the Spanish flu pandemic was a global killer. Estimates of the
dead range from 20-100 million, up to 5% of the population–all within
one year. Unlike previous flu pandemics and epidemics, this flu strain
killed healthy adults, whereas most flu strains targeted children, the
elderly, and the infirmed. More people died in this one-year pandemic
than the four years of the bubonic plague.

We often hear that many dangerous strains of influenza begin in China.
This belief is based on the dense population of humans living in close
proximity to high populations of animals. Many dangerous viral strains
have been found to originate in China jumping from birds or pigs to the
human population. Birds alone have been found to carry as many as 15
viral strains.

A virus is a pathogenic, parasitic organism that isn’t classified as
being alive, since a cell is an essential to our definition of life. A
virus has no cell membrane, no metabolism, no respiration and cannot
replicate outside of a living cell. A virus is a creepy half-live,
single strand or double strand of DNA or RNA or both, looking for a cell
to invade. Once inside, it reprograms the cell with its DNA or RNA and
multiplies on mass, bursting through the cell with a thousand or more
new virus strands seeking new cells to invade. RNA viruses mutate more
easily than DNA viruses. (SARS, bird flu, West Nile virus, swine flu,
hepatitis, measles, polio, yellow fever, and Ebola are among the many
RNA viruses).

If two viruses invade the same cell (a bird virus and a human virus, for
instance) their DNA can combine to form a new virus, a potentially
virulent one. The same is true if two animal viruses combine and jump
species to humans.

Viruses have two life cycles: the lytic cycle and the lysogenic cycle.

In the lytic cycle, the virus focuses on reproduction. It invades a
cell, inserts its DNA and creates thousands of copies of itself, bursts
through the cell membrane, killing the cell, and each new viral strand
invades new cells replicating the process.

In the lysogenic cycle, viruses remain dormant within its host cells.
The virus may remain dormant for years. Herpes and chickenpox are good
examples. (Chicken pox can cause shingles in later life when the dormant
virus reactivates.)

Our bodies fight off invading organisms, including viruses, all the
time. Our first line of defense is the skin, mucous, and stomach acid.
If we inhale a virus, mucous traps it and tries to expel it. If it is
swallowed, stomach acid may kill it. If the virus gets past the first
line of defense, the innate immune system comes into play. The
phagocytes wage war and release interferon to protect surrounding cells.
If they cannot destroy the invading force, the phagocytes call the
lymphocytes into play.

Our lymphocytes, T cells and B cells, retain a memory of any previous
infection that was serious enough to bring them into the battle.
Antibodies were formed and the body knows how to fight any infection it
recognizes. (This is how vaccinations work. The body has fought a
similar infection). But viruses can mutate, sometimes so much that they
body cannot recognize them as a similar infection they fought in the
past. They can also be so fast acting, they can kill before the
lymphocytes are brought into play.

Antiviral medications do not directly kill the virus; they trap it
within the cell, keeping it from reproducing. The only catch is that the
anti-viral has to be taken with 48 hours of symptom onset or it doesn’t
work.

Antibiotics don’t kill viruses. They kill bacteria, not viruses. And
they kill good bacteria that we need to keep our gut in balance. Taking
antibiotics when you have a viral infection can cause an immediate
overgrowth of Candida, giving the immune system an additional
system-wide infection to deal with when it needs all of its resources to
fight a viral infection.

Conventional treatment is supportive treatment–fluids, medications for
symptoms (such as asthma medication), but no medications have ever been
developed to kill the virus itself.

Don’t panic. Most viruses don’t affect us. But still, it brings up a
point. Viral infections are a symptom of a weak immune system. Your
immune system is wholly dependant on your gut health. A sick gut has an
abundance of fungi and other pathogens, and a healthy gut has a wide
variety of beneficial bacteria. The supplements listed below are a half
measure. A healthy nutrient dense diet, a healthy lifestyle, and a body
void of as many toxins as possible is the first and foremost defense. If
you want to skip the shortcuts and truly fortify your immune system,
read the following articles:

A healthy immune system begins in the gut with a healthy balance of
beneficial bacteria. For far too many Americans, Candida overgrowth
compromises the immune system, as it is constantly fighting the battle
to keep Candida in control.

If you do become ill, DO NOT feed the virus or the Candida with sugar.
Yes, you need to drink a lot of fluids, but don’t drink sodas and sugary
juices at this time. Cranberry lemonade sweetened with stevia is a good
choice. Try it warm or cold.

Gargle. Gargle. Gargle. Gargling lowers the viral load, leaving your
body with fewer invaders to replicate. Gargle with organic apple cider
vinegar. Even better, sip on this Mother Earth Organic Root Cider.
Cold’s and flu often start in the throat or the nasal cavities. At the
first sign of a sore throat or sinus infection, sip on the root cider!
If you don’t have it, use apple cider vinegar.

Also, remember that a fever is one of nature’s means to fight infection.
Of course, you don’t want it to get too high (higher than 102) and
drink plenty of fluids to prevent dehydration.

Vitamin A, vitamin D, vitamin E, and vitamin C are all vital nutrients
for the immune system. If you take high doses of vitamin C to fight a
virus, remember that you should not abruptly stop taking vitamin C. You
should titrate down. Vitamin C is needed by the immune system to make
interferon, which the immune system produces to protect healthy cells
from viral invasion.

Zinc has been proven to be effective against the common cold and to be
effective as a topical treatment for herpes sores. It is believed to be
effective due to preventing replication of the virus. The immune system
needs selenium to work properly and to build up the white blood cell
count.

Berberine is an alkaloid compound found in several different plants,
including European barberry, goldenseal, goldthread, Oregon grape,
Phellodendron, and Coptis chinensis. It has antibacterial,
anti-inflammatory, antiviral, anti-parasitic, and immune-enhancing
properties. It’s been proven effective against a vast array of bacteria,
protozoa, and fungi. It can be used topically on cuts and other wounds,
and it’s perhaps most commonly used to treat gastrointestinal issues.

Probiotics are always helpful in maintaining gut health, especially when
the body is under a viral attack that involves the digestive system.
Probiotic foods and drinks without added sugar can help maintain a
healthy balance of bacteria.

Garlic is anti-viral, anti-fungal, and antibacterial. You can take
garlic in a tonic or if you can handle it, chew raw garlic. It not only
will help fight the virus, it will help kill any secondary infections
trying to take root.

Echinacea not only supports the immune system, it also has been proven to reduce the severity and duration of viral infections.

Colloidal silver is believed to interfere with the enzymes that allow viruses (bacteria and fungi as well) to utilize oxygen.

A double-blind trail showed elderberry extract’s ability to reduce
symptoms of influenza and speed recovery. It also showed elderberry’s
ability to enhance immune response with higher levels of antibodies in
the blood. It is believed to inhibit a virus’s ability to penetrate
healthy cells and protect cells with powerful antioxidant S. Elderberry
has also been shown to inhibit replication in four strains of herpes
viruses and reduce infectivity of HIV strains.

The flavonoids in green tea are believed to fight viral infections by
preventing the virus from entering host cells and by inhibiting
replication.

Though double-blind clinical trials are needed, olive leaf extract has
been shown to inhibit replication of viruses. In one study, 115 of 119
patients had a full and rapid recovery from respiratory tract infections
while 120 of 172 had a full and rapid recovery from viral skin
infections such as herpes.

Pau d’arco has been used in indigenous medicine for generations. One of
its compounds, lapachol, has proven effective against various viruses,
including influenza, herpes simplex types I and II and poliovirus. It is
believed to inhibit replication.

Studies have shown that glycyrrhizin, a compound found in licorice root
was more effective in fighting samples of coronavirus from SARS patients
than four antiviral drugs. It reduces viral replication, cell
absorption, and the virus’s ability to penetrate cells. It is also being
used to treat HIV.

St. John’s Wort has been proven effective against influenza, herpes simplex, and HIV.

If you’re prone to viral infections or are dealing with a chronic
infection like HIV, as mentioned above, the first step is to get your
gut in shape. This is absolutely imperative. The best article to do that
with is Best Supplements To Kill Candida and Everything Else You Ever
Wanted To Know About Fungal Infections & Gut Health. Everyone who is
chronically ill has an abundance of Candida. Yes, everyone.

Provided your gut is healthy, or if you just feel the need to skip that
part, here are the supplements to take in order to make sure your immune
system is able to fight off viruses:

While there are most supplements listed above, the combination of these
listed here is more than enough to balance out the body and ward off
viral infection.